Question: Protein interaction network
gravatar for aj123
3.0 years ago by
United States
aj12380 wrote:


I have a list of genes for an organism. I want to pull out the first neighbor i.e the first protein/gene the organism is interacting with from the overall PPI network of the organism. Any suggestions on how I could do this?

cytoscape network protein ppi • 785 views
ADD COMMENTlink written 3.0 years ago by aj12380

"For an organism" is a bit limited in information. I could go ahead and suggest some databases with human protein interaction data, but that would likely not be what you want.

ADD REPLYlink written 3.0 years ago by WouterDeCoster39k

In which format do you have the graph defined in? Can you load the PPI into cytoscape? if it is not too long a list and the next step is manual inspection of annotations, then it can work. I think the best solution depends on the downstream analysis you want to perform, e.g. checking the annotations, looking at local network metrics of connected nodes, blasting the connected genes, GO term enrichment, looking up the genes in another network, etc.

ADD REPLYlink written 3.0 years ago by Michael Dondrup46k

enter image description hereThis is for Mouse data. Yes, I am able to load the entire PPI data into Cytoscape. The data is in this form (attached picture). Interactor A and B are the gene names.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by aj12380
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